Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_111392719.1 CLV31_RS09800 dihydrolipoyl dehydrogenase
Query= CharProtDB::CH_123536 (491 letters) >NCBI__GCF_003253485.1:WP_111392719.1 Length = 465 Score = 486 bits (1250), Expect = e-142 Identities = 248/461 (53%), Positives = 332/461 (72%), Gaps = 3/461 (0%) Query: 26 YDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHLLHQI 85 YDV+VIG GPGGYVAAI+AAQLG+ TA +EK LGGTCLNVGCIPSK+LL++S H Sbjct: 2 YDVIVIGSGPGGYVAAIRAAQLGMKTAIVEKYSTLGGTCLNVGCIPSKALLDSSEHYHNA 61 Query: 86 QHEAKERGISIQGEVGVDFPKLMAAKEKAVKQLTGGIEMLFKKNKVDYLKGAGSFVNEKT 145 H K GI+++ ++ VD ++++ K+ VKQ GI+ L KKNK+D G GSFV+ T Sbjct: 62 AHTFKTHGINLK-DLKVDLAQMISRKDDVVKQNVDGIQFLMKKNKIDVHHGLGSFVDAHT 120 Query: 146 VKVTPIDGSEAQEVEADHIIVATGSEPTPFPGIEIDEERIVTSTGILSLKEVPERLAIIG 205 VKVT DGS + +++ +II+ATGS+P P I++D++R++TST L +KE+P+ L +IG Sbjct: 121 VKVTKEDGSSS-DIQGKNIIIATGSKPASLPFIKLDKDRVITSTEALKMKEIPKHLIVIG 179 Query: 206 GGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLDFKLGTKVVKG 265 GG+IG+E+ SVY RLG+KV+V+EF ++I MD + K+ QK L K G DF L KV Sbjct: 180 GGVIGMELGSVYGRLGAKVSVVEFMDSIIPTMDKTMGKELQKSLKKLGFDFYLKHKVTAV 239 Query: 266 ERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKGRLIIDDQ 325 E G+ V ++ ++ K G+ +++ D +LV+IGR+P+T+GLN EA G++ ++G++ ++D Sbjct: 240 ENTGKEVVVKADNGK-GETIEIKGDYVLVSIGRKPYTDGLNAEAAGVKLTDRGQVEVNDH 298 Query: 326 FKTKHDHIRVIGDVTFGPMLAHKAEEEGIAAAEYIKKGHGHVNYANIPSVMYTHPEVAWV 385 +T HI IGDV G MLAHKAEEEG+ AE I H+NY IP V+YT PEVA V Sbjct: 299 LQTSVPHIYAIGDVVKGAMLAHKAEEEGVYVAETIAGQKPHINYLLIPGVVYTWPEVAAV 358 Query: 386 GLNEEQLKEQGIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVLGVHIIGPNAGE 445 G EEQLKEQG KYKVGKFPF+A+ RA+ +MDTDG VK +ADAET +LGVH+IGP + Sbjct: 359 GYTEEQLKEQGRKYKVGKFPFLASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTAD 418 Query: 446 MIAEAGLALEYGASTEDISRTCHAHPTLSEAFKEAALATFD 486 MIAEA +A+EY AS EDISR HAHPT +EAFKEA LA D Sbjct: 419 MIAEAVVAMEYRASAEDISRMSHAHPTYTEAFKEACLAATD 459 Lambda K H 0.316 0.135 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 609 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 491 Length of database: 465 Length adjustment: 34 Effective length of query: 457 Effective length of database: 431 Effective search space: 196967 Effective search space used: 196967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_111392719.1 CLV31_RS09800 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01350.hmm # target sequence database: /tmp/gapView.2837065.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01350 [M=461] Accession: TIGR01350 Description: lipoamide_DH: dihydrolipoyl dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-185 601.0 11.2 7.8e-185 600.9 11.2 1.0 1 NCBI__GCF_003253485.1:WP_111392719.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003253485.1:WP_111392719.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 600.9 11.2 7.8e-185 7.8e-185 1 457 [. 1 460 [. 1 465 [] 0.98 Alignments for each domain: == domain 1 score: 600.9 bits; conditional E-value: 7.8e-185 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieve 71 +ydv+viG+GpgGYvaAiraaqlg+k+a+vek ++lGGtClnvGCiP+KalL s+e ++++ + +k++gi+++ NCBI__GCF_003253485.1:WP_111392719.1 1 MYDVIVIGSGPGGYVAAIRAAQLGMKTAIVEKySTLGGTCLNVGCIPSKALLDSSEHYHNAAHtFKTHGINLK 73 59******************************99*************************************** PP TIGR01350 72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143 ++k+dl+++ rk+ vvk+ v+G+++L+kknk++v++G ++++d+++v+v+ke+++ + ++ kniiiAtGs+p NCBI__GCF_003253485.1:WP_111392719.1 74 DLKVDLAQMISRKDDVVKQNVDGIQFLMKKNKIDVHHGLGSFVDAHTVKVTKEDGSsSDIQGKNIIIATGSKP 146 *****************************************************988799************** PP TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216 ++lp+ ++ d+++vits+eal++ke+p++l+++GgGviG+E++s++ +lG+kv+v+e++d i+p++d+++ k+ NCBI__GCF_003253485.1:WP_111392719.1 147 ASLPF-IKLDKDRVITSTEALKMKEIPKHLIVIGGGVIGMELGSVYGRLGAKVSVVEFMDSIIPTMDKTMGKE 218 *****.8888888************************************************************ PP TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287 l+k+lkk g +++ ++kvt+ve++ +evvv+a+++ e+ ++++++vLv++Grkp +++l+ e+ gv+l++rg NCBI__GCF_003253485.1:WP_111392719.1 219 LQKSLKKLGFDFYLKHKVTAVENTGKEVVVKADNGkgETIEIKGDYVLVSIGRKPYTDGLNAEAAGVKLTDRG 291 *****************************88766536888899****************************** PP TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360 +++v+++l+t+vp+iyaiGDv++++mLAh+A++egv++ae+iag+++ +i+y ++P v+yt Peva+vG+tee NCBI__GCF_003253485.1:WP_111392719.1 292 QVEVNDHLQTSVPHIYAIGDVVKGAMLAHKAEEEGVYVAETIAGQKP-HINYLLIPGVVYTWPEVAAVGYTEE 363 ********************************************998.9************************ PP TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433 q+ke+g ++kvgkfpf a+g+a+a+ +tdG+vkv++d +t+eilG+h++g++ +++i+e+++a+e ++++e++ NCBI__GCF_003253485.1:WP_111392719.1 364 QLKEQGRKYKVGKFPFLASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIAEAVVAMEYRASAEDI 436 ************************************************************************* PP TIGR01350 434 aktihpHPtlsEaikeaalaalgk 457 +++ h+HPt++Ea+kea+laa+++ NCBI__GCF_003253485.1:WP_111392719.1 437 SRMSHAHPTYTEAFKEACLAATDN 460 *******************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (465 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.79 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory